Package

Foreword

Questions and bugs

For bugs, typos, suggestions or other questions, please file an issue
in our tracking system (https://github.com/sgibb/topdownr/issues)
providing as much information as possible, a reproducible example and
the output of sessionInfo().

If you don’t have a GitHub account or wish to reach a broader audience
for general questions about proteomics analysis using R, you may want
to use the Bioconductor support site: https://support.bioconductor.org/.

1 Introduction

1.1 The topdownr Data Generation Workflow

Data Generation Workflow

2 Installation of Additional Software

2.1 Setup the Thermo Software

To create methods the user will have to install and modify Orbitrap Fusion
LUMOS workstation first:

Request OrbitrapFusionLumosWorkstation.exe from Thermo Scientific.

Install the workstation by running OrbitrapFusionLumosWorkstation.exe.

Run
C:\Thermo\Instruments\TNG\OrbitrapFusionLumos\2.1\System\programs\TNGInstrumentConfigControl.exe,
set Optional Ion Source to ETD and Internal Calibration,
click Apply and OK (you could ignore the restart your instrument
message).

3 Creating Methods

Importantly, XMLmethodChanger does not create methods de novo, but modifies
pre-existing methods (supplied with XMLMethodChanger) using modifications
described in XML files. Thus the whole process of creating user specified
methods consists of 2 parts: